Evaluating the impact of U.S. Historical Climatology Network homogenization using the U.S. Climate Reference Network

Numerous inhomogeneities including station moves, instrument changes, and time of observation changes in the U.S. Historical Climatological Network (USHCN) complicate the assessment of long-term temperature trends. Detection and correction of inhomogeneities in raw temperature records have been undertaken by NOAA and other groups using automated pairwise neighbor comparison approaches, but these have proven controversial due to the large trend impact of homogenization in the United States. The new U.S. Climate Reference Network (USCRN) provides a homogenous set of surface temperature observations that can serve as an effective empirical test of adjustments to raw USHCN stations. By comparing nearby pairs of USHCN and USCRN stations, we find that adjustments make both trends and monthly anomalies from USHCN stations much more similar to those of neighboring USCRN stations for the period from 2004 to 2015 when the networks overlap. These results improve our confidence in the reliability of homogenized surface temperature records

On the Qubit Routing Problem

We introduce a new architecture-agnostic methodology for mapping abstract quantum circuits to realistic quantum computing devices with restricted qubit connectivity, as implemented by Cambridge Quantum Computing\u27s t|ket> compiler. We present empirical results showing the effectiveness of this method in terms of reducing two-qubit gate depth and two-qubit gate count, compared to other implementations

Assessing recent warming using instrumentally homogeneous sea surface temperature records

Sea surface temperature (SST) records are subject to potential biases due to changing instrumentation and measurement practices. Significant differences exist between commonly used composite SST reconstructions from the National Oceanic and Atmospheric Administration’s Extended Reconstruction Sea Surface Temperature (ERSST), the Hadley Centre SST data set (HadSST3), and the Japanese Meteorological Agency’s Centennial Observation-Based Estimates of SSTs (COBE-SST) from 2003 to the present. The update from ERSST version 3b to version 4 resulted in an increase in the operational SST trend estimate during the last 19 years from 0.07° to 0.12°C per decade, indicating a higher rate of warming in recent years. We show that ERSST version 4 trends generally agree with largely independent, near-global, and instrumentally homogeneous SST measurements from floating buoys, Argo floats, and radiometer-based satellite measurements that have been developed and deployed during the past two decades. We find a large cooling bias in ERSST version 3b and smaller but significant cooling biases in HadSST3 and COBE-SST from 2003 to the present, with respect to most series examined. These results suggest that reported rates of SST warming in recent years have been underestimated in these three data sets

Carbohydrate structure: : the rocky road to automation

With the introduction of intuitive graphical software, structural biologists who are not experts in crystallography are now able to build complete protein or nucleic acid models rapidly. In contrast, carbohydrates are in a wholly different situation: scant automation exists, with manual building attempts being sometimes toppled by incorrect dictionaries or refinement problems. Sugars are the most stereochemically complex family of biomolecules and, as pyranose rings, have clear conformational preferences. Despite this, all refinement programs may produce high-energy conformations at medium to low resolution, without any support from the electron density. This problem renders the affected structures unusable in glyco-chemical terms. Bringing structural glycobiology up to ‘protein standards’ will require a total overhaul of the methodology. Time is of the essence, as the community is steadily increasing the production rate of glycoproteins, and electron cryo-microscopy has just started to image them in precisely that resolution range where crystallographic methods falter most

Structure and activity of the Streptococcus pyogenes family GH1 6-phospho β-glycosidase, Spy1599

The group A streptococcus Streptococcus pyogenes is the causative agent of a wide spectrum of invasive infections, including necrotizing fasciitis, scarlet fever and toxic shock syndrome. In the context of its carbohydrate chemistry, it is interesting that S. pyogenes (in this work strain M1 GAS SF370) displays a spectrum of oligosaccharide-processing enzymes that are located in close proximity on the genome but that the in vivo function of these proteins remains unknown. These proteins include different sugar transporters (SPy1593 and SPy1595), both GH125 -1,6- and GH38 -1,3-mannosidases (SPy1603 and SPy1604), a GH84 -hexosaminidase (SPy1600) and a putative GH2 -galactosidase (SPy1586), as well as SPy1599, a family GH1 `putative -glucosidase'. Here, the solution of the three-dimensional structure of SPy1599 in a number of crystal forms complicated by unusual crystallographic twinning is reported. The structure is a classical (/)8-barrel, consistent with CAZy family GH1 and other members of the GH-A clan. SPy1599 has been annotated in sequence depositions as a -glucosidase (EC 3.2.1.21), but no such activity could be found; instead, three-dimensional structural overlaps with other enzymes of known function suggested that SPy1599 contains a phosphate-binding pocket in the active site and has possible 6-phospho--glycosidase activity. Subsequent kinetic analysis indeed showed that SPy1599 has 6-phospho--glucosidase (EC 3.2.1.86) activity. These data suggest that SPy1599 is involved in the intracellular degradation of 6-phosphoglycosides, which are likely to originate from import through one of the organism's many phosphoenolpyruvate phosphotransfer systems (PEP-PTSs)

Automating tasks in protein structure determination with the Clipper Python module

Scripting programming languages provide the fastest means of prototyping complex functionality. Those with a syntax and grammar resembling human language also greatly enhance the maintainability of the produced source code. Furthermore, the combination of a powerful, machine-independent scripting language with binary libraries tailored for each computer architecture allows programs to break free from the tight boundaries of efficiency traditionally associated with scripts. In the present work, we describe how an efficient C++ crystallographic library such as Clipper can be wrapped, adapted and generalised for use in both crystallographic and electron cryo-microscopy applications, scripted with the Python language. We shall also place an emphasis on best practices in automation, illustrating how this can be achieved with this new Python module. This article is protected by copyright. All rights reserved

A reassessment of temperature variations and trends from global reanalyses and monthly surface climatological datasets

The ERA-Interim and JRA-55 reanalyses of synoptic data and several conventional analyses of monthly climatological data provide similar estimates of global-mean surface warming since 1979. They broadly agree on the character of interannual variability and the extremity of the 2015/2016 warm spell to which a strong El Niño and low Arctic sea-ice cover contribute. Nevertheless global and regional averages differ on various time-scales due to differences in data coverage and sea-surface temperature analyses; averages from those conventional datasets that infill where they lack direct observations agree better with the averages from the reanalyses. The latest warm event is less extreme when viewed in terms of atmospheric energy, which gives more weight to variability in the Tropics, where the thermal signal has greater vertical penetration and latent energy is a larger factor. Surface warming from 1998 to 2012 is larger than indicated by earlier versions of the conventional datasets used to characterize what the Fifth Assessment Report of the Intergovernmental Panel on Climate Change termed a hiatus in global warming. None of the datasets exhibit net warming over the Antarctic since 1979. Centennial trends from the conventional datasets, HadCRUT4 on the one hand and GISTEMP and NOAAGlobalTemp on the other, differ mainly because sea-surface temperatures differ. Infilling of values where direct observations are lacking is more questionable for the data-sparse earlier decades. Change since the eighteenth century is inevitably more uncertain than change over and after a modern baseline period. The latter is arguably best estimated separately for taking stock of actions to limit climate change, exploiting reanalyses and using satellite data to refine the conventional approach. Nevertheless, early in 2016 the global temperature appears to have first touched or briefly breached a level 1.5 °C above that early in the Industrial Revolution, having touched the 1.0 °C level in 1998 during a previous El Niño

Inositol 1,3,4,5,6-pentakisphosphate 2-kinase is a distant IPK member with a singular inositide binding site for axial 2-OH recognition

Inositol phosphates (InsPs) are signaling molecules with multiple roles in cells. In particular Graphic (InsP6) is involved in mRNA export and editing or chromatin remodeling among other events. InsP6 accumulates as mixed salts (phytate) in storage tissues of plants and plays a key role in their physiology. Human diets that are exclusively grain-based provide an excess of InsP6 that, through chelation of metal ions, may have a detrimental effect on human health. Ins(1,3,4,5,6)P5 2-kinase (InsP5 2-kinase or Ipk1) catalyses the synthesis of InsP6 from InsP5 and ATP, and is the only enzyme that transfers a phosphate group to the axial 2-OH of the myo-inositide. We present the first structure for an InsP5 2-kinase in complex with both substrates and products. This enzyme presents a singular structural region for inositide binding that encompasses almost half of the protein. The key residues in substrate binding are identified, with Asp368 being responsible for recognition of the axial 2-OH. This study sheds light on the unique molecular mechanism for the synthesis of the precursor of inositol pyrophosphates

Fragon: rapid high-resolution structure determination from ideal protein fragments

Correctly positioning ideal protein fragments by molecular replacement presents an attractive method for obtaining preliminary phases when no template structure for molecular replacement is available. This has been exploited in several existing pipelines. This paper presents a new pipeline, named Fragon, in which fragments (ideal α-helices or β-strands) are placed using Phaser and the phases calculated from these coordinates are then improved by the density-modification methods provided by ACORN. The reliable scoring algorithm provided by ACORN identifies success. In these cases, the resulting phases are usually of sufficient quality to enable automated model building of the entire structure. Fragon was evaluated against two test sets comprising mixed α/β folds and all-β folds at resolutions between 1.0 and 1.7 Å. Success rates of 61% for the mixed α/β test set and 30% for the all-β test set were achieved. In almost 70% of successful runs, fragment placement and density modification took less than 30 min on relatively modest four-core desktop computers. In all successful runs the best set of phases enabled automated model building with ARP/wARP to complete the structure

Structure of Tagatose-1,6-bisphosphate Aldolase. Insight into chiral discrimination, mechanism, and specificity of class II aldolases

Tagatose-1,6-bisphosphate aldolase (TBPA) is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phosphate to produce tagatose 1,6-bisphosphate. The high resolution (1.45 Å) crystal structure of the Escherichia coli enzyme, encoded by the agaY gene, complexed with phosphoglycolohydroxamate (PGH) has been determined. Two subunits comprise the asymmetric unit, and a crystallographic 2-fold axis generates the functional tetramer. A complex network of hydrogen bonds position side chains in the active site that is occupied by two cations. An unusual Na(+) binding site is created using a interaction with Tyr(183) in addition to five oxygen ligands. The catalytic Zn(2+) is five-coordinate using three histidine nitrogens and two PGH oxygens. Comparisons of TBPA with the related fructose-1,6-bisphosphate aldolase (FBPA) identifies common features with implications for the mechanism. Because the major product of the condensation catalyzed by the enzymes differs in the chirality at a single position, models of FBPA and TBPA with their cognate bisphosphate products provide insight into chiral discrimination by these aldolases. The TBPA active site is more open on one side than FBPA, and this contributes to a less specific enzyme. The availability of more space and a wider range of aldehyde partners used by TBPA together with the highly specific nature of FBPA suggest that TBPA might be a preferred enzyme to modify for use in biotransformation chemistry